copick logical picksin

utils

Filter picks to include only those inside a reference volume.

Plugin command — copick-utils

This command is provided by the copick-utils plugin, not copick core. Install it to make this command available:

pip install copick-utils

See the plugin system guide for details.

Filter picks to include only those inside a reference volume.

Usage

copick logical picksin [OPTIONS]

Description

The reference volume can be either a watertight mesh or a segmentation (provide exactly one via --ref-mesh or --ref-seg). Each input pick is tested against the volume and only those whose coordinates fall inside it are written to the output. This is the inverse of copick logical picksout, which keeps the picks that fall outside the volume instead.

URI Format

Picks: object_name:user_id/session_id
Meshes: object_name:user_id/session_id
Segmentations: name:user_id/session_id@voxel_spacing

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--run-names, -r`	text · multiple	—	Specific run names to process (default: all runs).
`--input, -i`	COPICK_URI	required	Input picks URI (format: object_name:user_id/session_id). Supports glob patterns.

Reference Options

Option	Type	Default	Description
`--ref-mesh, -rm`	COPICK_URI	—	Reference mesh URI (format: object_name:user_id/session_id). Supports glob patterns.
`--ref-seg, -rs`	COPICK_URI	—	Reference segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns.

Tool Options

Option	Type	Default	Description
`--workers, -w`	integer	`8`	Number of worker processes.

Output Options

Option	Type	Default	Description
`--output, -o`	COPICK_URI	required	Output picks URI. Supports smart defaults (e.g., "ribosome", "ribosome/my-session", or "/my-session"). Full format: object_name:user_id/session_id.

Examples

# Include only picks inside a reference mesh
copick logical picksin -i "ribosome:user1/all-001" -rm "boundary:user1/boundary-001" \
    -o "ribosome:picksin/inside-001"

# Include only picks inside a segmentation
copick logical picksin -i "ribosome:user1/all-001" -rs "mask:user1/mask-001@10.0" \
    -o "ribosome:picksin/inside-001"